User: Vitis

gravatar for Vitis
Vitis1.6k
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New York
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Joined:
7 years, 3 months ago
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A plant geneticist from a taxonomist and naturalist background. Now trying to bridge classic genetics and evolutionary biology with ever-expanding genomic data and bioinformatic tools.

Posts by Vitis

<prev • 194 results • page 1 of 20 • next >
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Answer: A: [mpileup] 1 samples in 1 input files Is it an error?
... One possible cause is that the default mpileup ignores the non-properly paired reads, which could mean sometimes all reads in the alignment get ignored. Adding -A option would override the default behavior and report non-properly paired reads. Also see the following link: http://seqanswers.com/foru ...
written 3 days ago by Vitis1.6k
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Comment: A: Alternative to VEP.
... One vote for SnpEff. The best thing of it is that you could supply your annotations in GFF3 format. ...
written 18 days ago by Vitis1.6k
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Comment: C: GLM to predict what SNP influences DNA-methylation
... Is there any particular reason or hypothesis suggesting that SNPs' effects on DNA methylation are local? I would guess methylation status in a region could well be influenced by variants very far away? ...
written 24 days ago by Vitis1.6k
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Comment: C: Orthomcl clusters to fasta
... Try using Bioperl SeqIO and Bio::DB::Fasta, so you don't have to re-invent the wheels handling FASTA files... ...
written 24 days ago by Vitis1.6k
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Answer: A: GO enrichment analysis using R
... I saw the same problem with the tutorial. I suspect the problem is with the "AnnotationDbi" package, or its incompatibility with WGCNA. I think the error message is saying there is no object or class called "Ontology" by AnnotationDbi. Indeed, this is true, there is no Ontology class in AnnotationDb ...
written 7 months ago by Vitis1.6k
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Answer: A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
... The easy way is to use something else to predict the effects of your SNPs and see whether the same thing happens (much more stop codons than expected). I'd suggest to give Ensembl VEP a try. ...
written 21 months ago by Vitis1.6k
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Comment: C: Error in pysamstats
... Did pysamstats imported properly? Can you test it in interactive mode of python? ...
written 22 months ago by Vitis1.6k
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Answer: A: error in json to flatfile.pl prpgram running in jbrowse.
... It is exactly what the error message says: the feature ENST00000473466 has a parent feature ENSG00000097021, and ENSG00000097021 is not in your GFF3. ...
written 22 months ago by Vitis1.6k
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Answer: A: splitting Multifasta File Into A *Smaller Multifasta File containing few sequenc
... Try using BioPerl or BioPython modules handling FASTA, you can create tools to do all kinds of manipulation to FASTA files. http://bioperl.org/howtos/SeqIO_HOWTO http://biopython.org/wiki/Documentation ...
written 22 months ago by Vitis1.6k
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Comment: C: comparing two tracks over intervals on the genome
... Well, the solution based on bedops below is perfectly fine for this type of problem, I usually create this type of data with seamless chromosome windows for data standardization and documentation purpose. Somewhere down the road, you may repetitively need these operations to intersect new data. The ...
written 22 months ago by Vitis1.6k

Latest awards to Vitis

Great Question 20 months ago, created a question with more than 5,000 views. For Mapping Rates From Bwa
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Scholar 21 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Good Answer 3.3 years ago, created an answer that was upvoted at least 5 times. For A: A Result From Mummer Alignment
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Housekeeping Gene Identifications
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Mapping Rates From Bwa
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Autobiographer 4.5 years ago, has more than 80 characters in the information field of the user's profile.
Guru 4.5 years ago, received more than 100 upvotes.
Centurion 4.5 years ago, created 100 posts.
Supporter 4.5 years ago, voted at least 25 times.
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Appreciated 6.5 years ago, created a post with more than 5 votes. For A: Rna-Seq Data Variant Calling
Teacher 6.5 years ago, created an answer with at least 3 up-votes. For A: Rna-Seq Data Variant Calling
Student 6.6 years ago, asked a question with at least 3 up-votes. For Genomic Read Mapping Biased Towards Coding Regions?
Appreciated 6.8 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: How To Convert Centimorgan To Base Pair
Teacher 6.9 years ago, created an answer with at least 3 up-votes. For A: A Result From Mummer Alignment
Teacher 7.0 years ago, created an answer with at least 3 up-votes. For A: What Are The 'Copy Number Detection' Tools Out There For Exome Capture Ngs Data.
Teacher 7.0 years ago, created an answer with at least 3 up-votes. For A: Rna-Seq Time Course Data
Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Appreciated 7.1 years ago, created a post with more than 5 votes. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!

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